[BioPython] script for clustal alignment format

[Brad Chapman]

[Apologies for my lateness in replying to this (and other) messages. I 
have been out-o'-the-country-without-internet-access for the last week 
and am trying to catch up]

Scott T. Kelley writes:
> In that same vein, I was hoping that
> someone could point me to a python script that changed clustal W alignment
> formats to some other type of file format such as Fasta. I could probably
> write my own, but I thought if one was available... Maybe all this is
> included in Biopython? If so, I'll work on getting that running.

As some people replied and mentioned, Biopython will do this, and
there is actually documentation on how to do it (yippee :-). If you
grab the tutorial, available in html and pdf format from
http://www.biopython.org/wiki/html/BioPython/BiopythonCode.html,
section 3.4 deals with alignment formats, and section 3.4.2
specifically deals with converting between formats (with an clustalw
-> fasta example).

This is all in CVS only, and not in a release yet. As people mentioned, it 
also requires Martel and all of it's associated stuff (for clustalw
format stuff).

If you have problems or questions, please don't hesitate to ask.

> Also I wanted to ask if you all are looking for more python code for
> biopython? I have a whole bunch of scripts I use for various tasks that
> might be of interest. What kinds of things are you looking for?

Everything :-). Seriously, if you have things and want to make them
available for use, ScriptCentral
(http://www.biopython.org/ScriptCentral.shtml) is for this. If you
want to integrate them with Biopython, just make a proposal to the
list about it.

Glad you are interested (and that we actually had code to do what you
want :-).

Brad